3GFY

Klebsiella pneumoniae BlrP1 with FMN and cyclic diGMP, no metal ions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5277protein in 5 mM cy-diGMP, 5 mM CaCl2, 25 mM Tris-HCl pH 8.0, 40 mM NaCl, 5 mM MgCl2, 2 mM EDTA, 2 mM DTE, 5% glycerol, reservoir 0.1 M Na-Ac buffer pH 4.5, 0.2 M Ca-acetate, 17-20%PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.43α = 90
b = 96.53β = 90
c = 127.07γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARMOSAIC 225 mm CCD2007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.98407SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.646.5696.40.10413.45.42502825028
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.796.40.3525.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.646.562502825028139099.410.259040.259040.257580.28577RANDOM26.859
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.67-1.731.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.988
r_dihedral_angle_3_deg14.245
r_dihedral_angle_4_deg12.604
r_dihedral_angle_1_deg5.691
r_angle_refined_deg1.368
r_scangle_it0.913
r_mcangle_it0.554
r_scbond_it0.521
r_mcbond_it0.318
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.988
r_dihedral_angle_3_deg14.245
r_dihedral_angle_4_deg12.604
r_dihedral_angle_1_deg5.691
r_angle_refined_deg1.368
r_scangle_it0.913
r_mcangle_it0.554
r_scbond_it0.521
r_mcbond_it0.318
r_nbtor_refined0.302
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.16
r_nbd_refined0.157
r_symmetry_vdw_refined0.134
r_chiral_restr0.073
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5874
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms154

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing